[gmx-users] About the parameter in em.mdp..
Dear users, I am running the simulation for 100 ns , 10 ns of each. I have limited space in my a/c. (5 GB). If i will give the frequency of nstxout, nstvout, and nstxtcout 4000 or 5000 steps for every 10 ns simulation, Is that okay for the analysis or it will too long for good simulation analysis. Pls give me some suggession... Thnx.. /Henry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About gromacs run...
Dear users,Happy new yera to all. I have just a very simple query..I am running a simulation for 100 ns. I have decided to run it by 10 ns step of each. In every run, the gromacs generated confout.gro file, the traj.trr, traj.xtc, md.log , ener.edr file, state.cpt etc. The next time when i run the simulation for the next 10 ns , I have edited the em.mdp file and just change the tinit to the last time that i was run and the nsteps to 500 for 10 ns. And the command i used for grompp is ... grompp -f em.mdp -c confout.gro -p topol.top -o topol.tpr And then it will generate the topol.tpr file. and the command is then mdrun My question is is that oaky ... or I have to use any more file in the grompp command like that traj.trr or state.cpt for tracking velocity?? Thnx... /HenryBiochemistry. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] calculaton of electrostatic potential
Hi all, I want to calculate the electrostatic potential of my simulated membrane system (DMPC). I think, I need to make an index file for this purpose. Isn't it? In that case, how could I make the selection, I mean i have to select the whole membrane group or I have to create an index file with some particular specific atoms? I need some idea to understand this. Could someone pls help me! Best regards, /Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate PN vector head group angle...
Hello gromacs experts, I want to calculate the PN vector angular distribution along the bilayer axis. I am currently using gromacs 4.0.5 version. Is there any tools in gromacs which one I can use to calculate this properties? If not, anyone pls tell me how can I proceed? I am actually quiet new. So I think I need some basic knowledge.. Thanks in advance /Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Fw: [gmx-users] gromacs..
Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, December 8, 2009 12:49:18 PM Subject: Re: [gmx-users] gromacs.. Henry Ynag wrote: > Hello everyone, > > I am quite new to gromacs. I would like to know how can I calculate the area > per lipid for my simulations. I am running simulations with 128 DMPC lipid > bilayer. I have the output of 30 ns simulations. Also how can i make a graph > with this output. > Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs..
Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, December 8, 2009 12:49:18 PM Subject: Re: [gmx-users] gromacs.. Henry Ynag wrote: > Hello everyone, > > I am quite new to gromacs. I would like to know how can I calculate the area > per lipid for my simulations. I am running simulations with 128 DMPC lipid > bilayer. I have the output of 30 ns simulations. Also how can i make a graph > with this output. > Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xmgrace plot
Hello Jon, Thnx. One more question. I have the output of every 10 ns simulation over 50 ns. For every 10 ns simulation step I have the .xvg file . Is there any way in xmgrace so that I can concatenate all the .xvg file from 0 to 50 ns simulation and show them one xmgrace graph Thanks again Henry From: Jon Fuller To: Discussion list for GROMACS users Sent: Tue, December 8, 2009 11:53:25 AM Subject: Re: [gmx-users] xmgrace plot >From the command line you can type xmgrace file1.xvg file2.xvg (where file1 >and file2 are the filenames!). Jon 2009/12/8 Henry Yang Hello everyone, > >I am also new to xmgrace. I have two .xvg file which I have got from the >simulation data analysis. How can I open both of them in one xmgrace graph >with two distinct color? How can I proceed with the comand? > >I know this is very basic but I have to learn! >Pls give me response. > >Henry >Biochemistry > > > >-- >>gmx-users mailing listgmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to gmx-users-requ...@gromacs.org. >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xmgrace plot
Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
